Protein-protein interaction Search Results

Protein-protein interaction

392 results

Protein-protein interaction

The presence of the NAC1-GAL4 activation domain fusion protein and the NAC1–GAL4 DNA binding domain fusion protein resulted in significantly more growth than the autoactivation seen with the latter alone (Fig. ​(Fig.3C),3C), suggesting that NAC1 can indeed dimerize

Protein-protein interaction

AtCAP1 ... The proline-rich stretch from amino acids 227 to 237 (Figure 1) may have the potential to bind to SH3 proteins because the conserved prolines at positions 7 and 10 match the consensus PXXP sequence (where X is any amino acid) that is involved in interaction with the SH3 domain. CAPs from other organisms also have one or two proline-rich sequences in the middle region, which is shown as an SH3 protein binding motif (Freeman et al., 1996

Protein-protein interaction

To further demonstrate the physical interaction between AtRbx1 and the AtCul1 protein, we performed pull-down assays. AtRbx1;1 was expressed in Escherichia coli as a translational fusion protein with GST. The purified GST-Rbx1 fusion protein (or GST alone as a control) was incubated with Arabidopsis crude protein extracts, and the bound plant proteins were immunoblotted with the AtCul1 antibody. AtCul1 co-purified with the GST-Rbx1 fusion protein but not with the GST protein alone

Protein-protein interaction

AtRbx1 was cloned into the pGBKT7 bait plasmid to produce a fusion protein with Gal4 DNA binding domain. Another small Arabidopsis RingH2 protein (49) not related to the primary protein sequence of AtRbx1 was also introduced into pGBKT7 plasmid. AtCul1 (At4g02570) and AtCul4 (At5g46210) were cloned into the prey pGADT7 vector to produce fusion proteins with the Gal4 activation domain. Only AtRbx1 and not the other small RingH2 protein interacted with the cullin proteins by the two-hybrid assay (Fig. 3 A). β-Galactosidase activities, used to quantify the protein interactions, indicated that the AtRbx1 interacts similarly with both AtCul1 and AtCul4 proteins (Fig.3 B

Protein-protein interaction

This experiment was also performed with another F-box protein that is closely related to TIR1 called leucine rich repeat F-box 1 (LRF1). As shown in Figure 6C, GST–RCE1 also pulled down LRF1-Myc from plant extracts. These results indicate that RCE1 interacts with complete SCF complexes

Dharmasiri S, Dharmasiri N, Hellmann H, Estelle M - The RUB/Nedd8 conjugation pathway is required for early development in Arabidopsis

Protein-protein interaction

we used 35S::Myc-RCE1 plants to determine whether GST–RBX1 interacts with Myc-RCE1. The results in Figure 6B show that GST–RBX1 interacts with Myc-RCE1 in plant extracts, consistent with our results using purified proteins

Dharmasiri S, Dharmasiri N, Hellmann H, Estelle M - The RUB/Nedd8 conjugation pathway is required for early development in Arabidopsis

Protein-protein interaction

First we asked whether AXR1 interacts with Myc-RCE1 by immunoprecipitating AXR1 from 35S::Myc-RCE1 seedlings. Figure 6D shows that Myc-RCE1 co-immunoprecipitates with AXR1, indicating that RCE1 forms a stable complex with AXR1

Dharmasiri S, Dharmasiri N, Hellmann H, Estelle M - The RUB/Nedd8 conjugation pathway is required for early development in Arabidopsis

Protein-protein interaction

To show that CUL is also present in a complex with RCE1, we immunoprecipitated CUL1 from extracts prepared from 35S::Myc-RCE1 seedlings. Immunoblotting with anti-Myc antibody revealed the presence of Myc-RCE1 in the immunoprecipitate

Dharmasiri S, Dharmasiri N, Hellmann H, Estelle M - The RUB/Nedd8 conjugation pathway is required for early development in Arabidopsis

Protein-protein interaction

To further confirm the physical interaction between AS1 and AS2 proteins, we performed ELISA experiments using purified His-AS1 and GST-AS2 (Fig. 8C). Our results showed that the increased absorbance could be recorded only in the presence of both AS1 and AS2 proteins (Fig. 8D), indicating these two proteins can indeed associate physically

Protein-protein interaction

We then immunoprecipitated HEN3-HA from these plants using an anti-HA monoclonal antibody and performed a kinase assay using E. coli produced, 6×His-tagged Arabidopsis CTD, 6×His-GFP and human Histone H1 as substrates. Anti-HA, but not the control anti-protein C immunoprecipitate, was able to phosphorylate 6×His-CTD, but not 6×His-GFP or human Histone H1

Wang W, Chen X - HUA ENHANCER3 reveals a role for a cyclin-dependent protein kinase in the specification of floral organ identity in Arabidopsis

Protein-protein interaction

To identify potential targets of the activated BRI1 receptor kinase in response to BR signal, we conducted a yeast two-hybrid screening using the kinase domain of BRI1 (BRI1CK) as the bait. Out of 96 positive BRI1-interacting clones, 60 were found to be derived from the same Arabidopsis gene (At5g58220) that encodes a hypothetical protein of 324 amino acids ... we deleted the N-terminal 29 amino acids to create a truncated TTL protein, TTLΔN29, and tested its interaction with the BRI1 kinase domain by the yeast two-hybrid assay. As shown in Table 1, TTLΔN29 failed to interact with BRI1CK, confirming that these 29 amino acids are crucial for the TTL–BRI1 interaction. To determine if such a 29–amino acid peptide is sufficient for binding to BRI1, we made a chimeric protein, TTLN29:BES1, by fusing the 29–amino acid peptide to BES1, a nuclear BR signaling protein that does not interact with BRI1 (Yin et al., 2002; Zhao et al., 2002). The resulting chimeric protein was then tested by the yeast two-hybrid assay for its interaction with BRI1CK. As shown in Table 1, the TTLN29:BES1 fusion protein did not interact with BRI1CK in yeast cells. These results indicated that whereas the N-terminal 29 amino acids are essential for the TTL–BRI1 interaction, they are not sufficient to bind BRI1 ... Using the yeast two-hybrid assay, we also tested the interaction between TTL with three mutated BRI1CK, each containing a unique single amino acid change that was identified in three mutant bri1 alleles (bri1-101 changes Glu1078 to Lys, bri1-104 mutates Ala1031 to Thr, and bri1-115 substitutes Gly1048 with Asp). Whereas all three bri1 mutations were known to destroy the in vivo function of BRI1 (Li and Chory, 1997), they have different effects on the BRI1 kinase activity. As shown in Figure 2A, bri1-101 completely eliminates and bri1-115 greatly reduces the autophosphorylation activity of an E. coli–expressed glutathione S-transferase (GST)-BRI1CK fusion protein, whereas bri1-104 mutation reduces the kinase activity of GST-BRI1CK by only ∼50%. Results shown in Figure 2B revealed that an active kinase activity was required for the BRI1–TTL interaction. Both bri1-101 and bri1-115 mutations completely abrogate the BRI1–TTL interaction. By contrast, the BRI1CK containing the bri1-104 mutation can still interact with TTL to the same extent as the wild-type BRI1CK

Protein-protein interaction

The fact that only the kinase active BRI1CKs were capable of interacting with TTL prompted us to investigate whether TTL might be a substrate for the BRI1 kinase. We fused the full-length TTL with the maltose binding protein (MBP) and expressed the resulting fusion protein in E. coli. After purification, the MBP-TTL fusion protein was mixed with the wild type or the bri1-101–mutated GST-BRI1CK fusion protein and assayed protein phosphorylation. As shown in Figure 2C, the wild-type GST-BRI1CK fusion protein exhibited strong autophosphorylation activity in vitro, whereas no autophosphorylation was detected for the MBP-TTL fusion protein. However, TTL was phosphorylated when the two fusion proteins were mixed together in the kinase assay solution. Because of the similar electrophoretic mobility of the two fusion proteins, only one-fifth of the GST-BRI1CK of the autophosphorylation assay was used in the transphosphorylation assay to clearly reveal the phosphorylated MBP-TTL band. When incubated with the kinase-dead GST-BRI1CK fusion protein, no phosphorylation of TTL was detected, eliminating the possibility that the observed TTL phosphorylation was catalyzed by an unknown E. coli kinase that might be copurified with the GST-BRI1CK fusion protein. No transphosphorylation was detected when the GST-BRI1CK fusion protein was incubated with the MBP alone. Taken together, these in vitro phosphorylation results indicated that BRI1 could phosphorylate TTL in vitro

Protein-protein interaction

The GRF1 protein was retained only on the GST-GIF1 column but not on a GST column (Fig. 3A), confirming direct interaction between GRF1 and GIF1. Among the fragments containing the QLQ, WRC, or C-terminal domains of GRF1, only that containing the QLQ domain was able to bind to GIF1 (Fig. 3B). Only the SNH but not the QG domain of GIF1 was able to bind GRF1

Protein-protein interaction

Complementing the yeast two-hybrid data, we also observed a weak coimmunoprecipitation of eIF3h with the CSN subunits CSN4 and CSN5 ... The interaction with CSN4 and CSN5 may be indirect (i.e., mediated by an interaction with CSN1, CSN7, or CSN8

Protein-protein interaction

Complementing the yeast two-hybrid data, we also observed a weak coimmunoprecipitation of eIF3h with the CSN subunits CSN4 and CSN5 ... The interaction with CSN4 and CSN5 may be indirect (i.e., mediated by an interaction with CSN1, CSN7, or CSN8

Protein-protein interaction

Next, coimmunoprecipitation experiments with wild-type Arabidopsis seedling extracts using an antiserum generated against eIF3h demonstrated an interaction between eIF3h and two other eIF3 subunits, the core subunit, eIF3b, and the noncore subunit, eIF3e (Figure 6B), confirming that eIF3h is an eIF3 subunit

Protein-protein interaction

Furthermore, in line with the copurification of eIF3h with the cauliflower CSN (Karniol et al., 1998), eIF3h interacted directly with Arabidopsis CSN1, CSN7, and CSN8 in yeast (Figure 6A) but not with CSN4 or CSN5 (data not shown

Protein-protein interaction

Furthermore, in line with the copurification of eIF3h with the cauliflower CSN (Karniol et al., 1998), eIF3h interacted directly with Arabidopsis CSN1, CSN7, and CSN8 in yeast (Figure 6A) but not with CSN4 or CSN5 (data not shown

Protein-protein interaction

Furthermore, in line with the copurification of eIF3h with the cauliflower CSN (Karniol et al., 1998), eIF3h interacted directly with Arabidopsis CSN1, CSN7, and CSN8 in yeast (Figure 6A) but not with CSN4 or CSN5 (data not shown

Protein-protein interaction

Next, coimmunoprecipitation experiments with wild-type Arabidopsis seedling extracts using an antiserum generated against eIF3h demonstrated an interaction between eIF3h and two other eIF3 subunits, the core subunit, eIF3b, and the noncore subunit, eIF3e (Figure 6B), confirming that eIF3h is an eIF3 subunit

Protein-protein interaction

Protein-protein interaction

Since mammalian CUL1 is known to interact with CAND1 (Liu et al., 2002; Zheng et al., 2002; Hwang et al., 2003; Oshikawa et al., 2003), we generated a recombinant Glutathione-S-transferase-HVE (GST-HVE) protein that was used in pull-down experiments. CUL1 was translated in vitro in rabbit reticulocyte lysate in the presence of 35S-Met and then incubated with GST or GST-HVE. As shown by SDS-PAGE gel autoradiography (see Fig. S2A in the supplementary material), GST-HVE, but not GST, was able to interact with CUL1

Protein-protein interaction

To substantiate that AtNAP1;1 is a substrate for PFT, protein extracts from wild-type or era1-1 flowers were tested as a source for the enzyme (Fig. 1B). AtNAP1;1 but not AtNAP1;1C369S was labeled in the presence of protein extracts from wild-type flowers, confirming that the protein extract had PFT activity and that AtNAP1;1 could be correctly farnesylated at the Cys acceptor in the CKQQ prenylation motif. The protein extract from era1-1 flowers was unable to farnesylate AtNAP1;1, confirming the lack of PFT activity in the mutant and establishing that AtNAP1;1 is a substrate of PFT. To confirm that AtNAP1;1 is also farnesylated in vivo, we expressed green fluorescent protein (GFP)-AtNAP1;1 and GFP-AtNAP1;1C369S in tobacco BY-2 cells under control of the cauliflower mosaic virus (CaMV) 35S promoter. Soluble proteins from cells labeled with [3H]mevalonic acid were extracted and separated on SDS-polyacrylamide gels, which were then used either for immunoblot analysis with a polyclonal NAP1 antibody or for fluorography to detect labeled GFP-AtNAP1;1 (Fig. 1C). GFP-AtNAP1;1 and GFP-AtNAP1;1C369S were expressed to a similar level in BY-2 cells. A labeled protein corresponding to the size of GFP-AtNAP1;1 was detected only in extracts from cells expressing GFP-AtNAP1;1 but not in cells expressing GFP-AtNAP1;1C369S or in control BY-2 cells. Together, these results establish that AtNAP1;1 is efficiently farnesylated in vivo as well

Protein-protein interaction

To test if AtNAP1;1 can be prenylated by PFT, we incubated the purified protein with recombinant Arabidopsis PFT and [3H]FPP. AtNAP1;1 was labeled strongly in the presence of both PFT and [3H]FPP but not with PGGT-I using either [3H]FPP or [3H]GGPP (Fig. 1A). AtNAP1;1 was also labeled weakly by PFT using [3H]GGPP, because the enzyme is somewhat promiscuous for GGPP (Trueblood et al., 1993; Lane and Beese, 2006). Mutation of the conserved Cys farnesyl acceptor in the CKQQ motif to Ser (AtNAP1;1C369S) confirmed that farnesylation required a functional farnesylation motif

Protein-protein interaction

To examine whether Arabidopsis SKB1 methylates histone arginines, we assayed in vitro a GST-SKB1 fusion protein, purified by affinity chromatography from Escherichia coli, for methylation activity, with histones and myelin basic protein (MBP) used as substrates. Both histone and MBP were methylated, but of the five histones (H1, H2A, H2B, H3 and H4), only H4 was methylated (Figure 4F). We then used specific antibodies to examine whether SKB1 methylates H4R3. GST-SKB1 catalyzed H4R3 symmetric dimethylation (H4R3sme2) but not asymmetric dimethylation (Figure 4G), which suggests that SKB1 can symmetrically methylate H4R3 as does PRMT5

Protein-protein interaction

To show that the VFB proteins have retained the ability to bind SKP1 proteins, we used VFB2 as a representative family member to examine its interaction with ARABIDOPSIS SKP1-2 (ASK2), a predominant member of the Arabidopsis SKP1 protein family, using the yeast two-hybrid system (Risseeuw et al., 2003; Zhao et al., 2003). Our analysis revealed an interaction between VFB2 and ASK2 but not between VFB2 and the two other SCF complex components RBX1 and CUL1

Protein-protein interaction

We therefore performed a yeast two-hybrid screen with MID as bait to identify interacting proteins. One of the found putative interactors, RHL1, was particularly interesting as the mid and rhl1 mutants show an identical phenotype

Protein-protein interaction

To test further the hypothesis that MID is a component of the topoisomerase VI complex, we tested interactions between MID and RHL1 by directed yeast two-hybrid assay and the bimolecular fluorescence complementation assay (BiFC; Walter et al., 2004). Directed yeast two-hybrid assays confirmed the MID–RHL1 interaction found in the yeast two-hybrid screen (data not shown). To independently verify MID–RHL1 interactions by BiFC, we cotransformed plasmids encoding BiFC fusion constructs of the two proteins with the N- or C-terminal part of YFP into Arabidopsis protoplasts. A restored YFP fluorescence was localized in the nuclei of transfected protoplasts, suggesting that MID and RHL1 can interact in planta

Protein-protein interaction

To substantiate that MID and RHL1 are components of the topoisomerase VI complex in planta, coimmunoprecipitation (Co-IP) experiments were performed. We created transgenic plants harboring the 35S:RHL1-cyan fluorescent protein (CFP) and 35S:HA-RHL2 constructs and transgenic plants harboring the 35S:RHL1-CFP and 35S:HA-MID constructs. In these experiments, we could not detect the HA-MID protein in Co-IP experiments with the MID and RHL1 proteins with anti-HA beads (data not shown). However, we found that HA-RHL2 protein was immunoprecipitated with anti-GFP beads and RHL1-CFP with anti-HA beads from the plants harboring the 35S:RHL1-CFP and 35S:HA-RHL2 constructs

Protein-protein interaction

We have previously established the CTD phosphatase activities of CPL1 ... using CTD tetraheptad phosphopeptide substrates and a GST-CTD fusion protein that was phosphorylated by mouse ERK2 (Koiwa et al. 2004

Protein-protein interaction

A fragment of ARF2 was isolated as a BIN2-interacting protein. The ARF2 region interacting with BIN2 is restricted to the 540 aa in C terminus, encompassing the ARF-Aux/IAA dimerization domain (28, 29). A full-length ARF2 clone was independently verified to interact with BIN2 (Fig. 2A

Protein-protein interaction

AtORC1a ... complete open-reading frame was assayed in a two-hybrid screen against an Arabidopsis cDNA two-hybrid library. Among the interacting proteins, a novel 737-amino-acid protein (At5g13060) of approximately 81 kDa was identified ... Yeast two-hybrid assays revealed that ABAP1 interaction with AtORC1a was mediated by the ARM repeats and by AtORC1a N terminus (amino acids 1–341) that contained the BAH and PHD domains

Protein-protein interaction

To unravel protein complexes in which ABAP1 takes part, a yeast two-hybrid screen under high stringency selection conditions was performed with an Arabidopsis cDNA library as a bait. Several transcription factors, belonging to the NAC, AP2 and TCP families (unpublished results) were identified. One of the ABAP1-associated transcription factors was AtTCP24 (At1g30210) that belongs to the class-II TCP transcription factor family (Cubas et al, 1999), the members of which negatively regulate plant cell proliferation and leaf morphogenesis

Protein-protein interaction

In vivo interaction was observed in immunoprecipitation experiments of protein extracts of Arabidopsis cell suspension LMM-1 protoplasts that produced ABAP1 and AtTCP24–FLAG, with the anti-ABAP1 antibody

Protein-protein interaction

To confirm the specific interaction in planta, a bimolecular fluorescence complementation assay was performed using full-length HUB1 and MED21. HUB1 was translationally fused with the N-terminal 155–amino acid portion of the yellow fluorescent protein (YFP) (pHUB1-cYFP), and MED21 was fused with the C-terminal 86–amino acid portion of YFP (pMED21-nYFP). pHUB1-cYFP and pMED21-nYFP were cotransformed into Nicotiana benthamiana leaves through agroinfiltration. YFP fluorescence was observed only when the two constructs were coexpressed (Figure 9B, top row). Leaves from plants infiltrated with either of the constructs alone, or in combination with the empty vector, did not show any YFP fluorescence (Figure 9B, middle and bottom rows). Staining of cells with the fluorescent nuclear stain 4',6-diamidino-2-phenylindole (DAPI) revealed fluorescence in the nucleus of cells cotransformed with both constructs, indicating interactions in the nucleus. The interaction of HUB1 and MED21 in the nucleus is consistent with the function of HUB1 in histone monoubiquitination and the function of MED21 as a transcriptional coregulator

Protein-protein interaction

To gain further insights into the mechanisms of HUB1 function, we screened for HUB1 interacting proteins using a yeast two-hybrid screen. MED21 (At4g04780), a homolog of human and yeast MED21, constituents of the Mediator complex involved in transcriptional regulation (Bjorklund and Gustafsson, 2005), was identified as a strong interactor of HUB1

Protein-protein interaction

Next, we tested for potential interactions between the BOP1, BOP2, and bop1-1 proteins. In the yeast two-hybrid system, BOP1 and BOP2 protein fused to the Gal4 DNA BD showed autoactivation activity when tested with the control empty vector (E) containing the activation domain (AD). Nonetheless, we could clearly detect pairwise interactions between the BOP1, BOP2, and bop1-1 proteins (Figure 1C). The BOP1 and BOP2 proteins showed equally strong interactions as homodimers and heterodimers

Protein-protein interaction

Next, we tested for potential interactions between the BOP1, BOP2, and bop1-1 proteins. In the yeast two-hybrid system, BOP1 and BOP2 protein fused to the Gal4 DNA BD showed autoactivation activity when tested with the control empty vector (E) containing the activation domain (AD). Nonetheless, we could clearly detect pairwise interactions between the BOP1, BOP2, and bop1-1 proteins (Figure 1C). The BOP1 and BOP2 proteins showed equally strong interactions as homodimers and heterodimers

Protein-protein interaction

Next, we tested for potential interactions between the BOP1, BOP2, and bop1-1 proteins. In the yeast two-hybrid system, BOP1 and BOP2 protein fused to the Gal4 DNA BD showed autoactivation activity when tested with the control empty vector (E) containing the activation domain (AD). Nonetheless, we could clearly detect pairwise interactions between the BOP1, BOP2, and bop1-1 proteins (Figure 1C). The BOP1 and BOP2 proteins showed equally strong interactions as homodimers and heterodimers

Protein-protein interaction

Y2H with a JAZ1 deletion series revealed that NINJA was only capable of binding JAZ1 fragments containing the TIFY motif ... A deletion series of NINJA was constructed (Fig. 1c) and tested for JAZ1 interaction, demonstrating that the C domain of NINJA was responsible and sufficient for JAZ protein interaction. Finally, the 39 amino-acid protein fragment harbouring the TIFY motif of JAZ1 directly interacted with the C domain of NINJA

Protein-protein interaction

To provide further evidence for such interaction, co-immunoprecipitation experiments were performed using total Arabidopsis leaf protein extraction treated with DNase. Our result showed that SIG6 protein could be precipitated by DG1 antibody, but not by pre-serum (Figure 1c). These results suggested that the interaction of DG1 with SIG6 occurs in vivo

Protein-protein interaction

To obtain further insight into the function of DG1, a yeast two-hybrid screen was performed to identify its interacting proteins. Fusion of the N-terminal 47 amino acids to GFP revealed that it can be imported to the chloroplast (Figure S1). The DG1 protein lacking amino acids 1–47 of the N-terminal region was used as the bait, and 33 positive clones were selected from 2 × 106 colonies with the Arabidopsis random cDNA expression library. Sequence analysis of the recovered selected clones revealed that eight of the 33 putative interacting preys contained two independent cDNAs of different sizes from the SIG6 gene. Of the eight clones, six cDNAs encoded 2–547 amino acids of the SIG6 protein, whereas the two others encoded 32–547 amino acids. These results indicate that SIG6 is a prevalent DG1-interacting partner in the yeast two-hybrid screen

Protein-protein interaction

To confirm the interaction between DG1 and SIG6 in plant cells, we performed bimolecular fluorescence complementation (BiFC) analysis in the protoplasts of Arabidopsis leaf mesophyll cells (Citovsky et al., 2006). In this assay, DG1 and SIG6 were fused to inactive N-terminal and C-terminal moieties of yellow fluorescent protein (YFP), respectively, and were co-delivered into leaf mesophyll protoplasts in Arabidopsis. Our results showed that YFP fluorescence was observed in the chloroplast of the protoplasts, and merged with the autofluorescence of chlorophylls

Protein-protein interaction

To establish whether the physical interaction also occurs in plant cells, a bimolecular fluorescence complementation system (BiFC; Citovsky et al., 2006) was used in combination with an Arabidopsis leaf mesophyll protoplast transient expression assay (Yoo et al., 2007). Again, positive interactions were detected for each pair of RACK1 and eIF6 proteins (Fig. 4B). The interaction was primarily detected in the cytoplasm and nucleus, which is consistent with the respective subcellular localization of each protein

Protein-protein interaction

To establish whether the physical interaction also occurs in plant cells, a bimolecular fluorescence complementation system (BiFC; Citovsky et al., 2006) was used in combination with an Arabidopsis leaf mesophyll protoplast transient expression assay (Yoo et al., 2007). Again, positive interactions were detected for each pair of RACK1 and eIF6 proteins (Fig. 4B). The interaction was primarily detected in the cytoplasm and nucleus, which is consistent with the respective subcellular localization of each protein

Protein-protein interaction

To establish whether the physical interaction also occurs in plant cells, a bimolecular fluorescence complementation system (BiFC; Citovsky et al., 2006) was used in combination with an Arabidopsis leaf mesophyll protoplast transient expression assay (Yoo et al., 2007). Again, positive interactions were detected for each pair of RACK1 and eIF6 proteins (Fig. 4B). The interaction was primarily detected in the cytoplasm and nucleus, which is consistent with the respective subcellular localization of each protein

Protein-protein interaction

To establish whether the physical interaction also occurs in plant cells, a bimolecular fluorescence complementation system (BiFC; Citovsky et al., 2006) was used in combination with an Arabidopsis leaf mesophyll protoplast transient expression assay (Yoo et al., 2007). Again, positive interactions were detected for each pair of RACK1 and eIF6 proteins (Fig. 4B). The interaction was primarily detected in the cytoplasm and nucleus, which is consistent with the respective subcellular localization of each protein

Protein-protein interaction

To establish whether the physical interaction also occurs in plant cells, a bimolecular fluorescence complementation system (BiFC; Citovsky et al., 2006) was used in combination with an Arabidopsis leaf mesophyll protoplast transient expression assay (Yoo et al., 2007). Again, positive interactions were detected for each pair of RACK1 and eIF6 proteins (Fig. 4B). The interaction was primarily detected in the cytoplasm and nucleus, which is consistent with the respective subcellular localization of each protein

Protein-protein interaction

To establish whether the physical interaction also occurs in plant cells, a bimolecular fluorescence complementation system (BiFC; Citovsky et al., 2006) was used in combination with an Arabidopsis leaf mesophyll protoplast transient expression assay (Yoo et al., 2007). Again, positive interactions were detected for each pair of RACK1 and eIF6 proteins (Fig. 4B). The interaction was primarily detected in the cytoplasm and nucleus, which is consistent with the respective subcellular localization of each protein

Protein-protein interaction

In a yeast two-hybrid (Y2H) assay, PAR1 has been shown to be able to homodimerize ... Therefore we used this technique to test the dimerization ability of truncated PAR1 versions that contain the HLH domain (AHC, HC, NAH and AH) (Figure 5a). The deletion fragments were fused to the GAL4 activation domain (AD) and tested for dimerization against full-length PAR1 fused to the GAL4 DNA-binding domain (BD-PAR1). Only yeast colonies co-expressing AD-PAR1, AD-AHC or AD-HC together with BD-PAR1 grew in SD-AHLT medium (Figure 5a). These results indicated that the interaction was taking place only when both HLH and C-terminal domains were present

Protein-protein interaction

To confirm a direct interaction between AtNUFIP and At15.5K, we fixed a glutathione S-transferase (GST)-At15.5K recombinant protein to glutathione-sepharose beads to trap in vitro translated [35S]-Met-AtNUFIP. Bound and unbound products were analyzed by SDS-PAGE and revealed by autoradiography. [35S]-Met-AtNUFIP is highly susceptible to proteolysis and gives three major bands of approximately 50 kDa (Figure 3b). These bands were significantly enriched in the GST-At15.5K bound fraction and were not retained on control glutathione-GST beads (Figure 3b). These results confirm that AtNUFIP directly interacts with At15.5K and could be implicated in C/D snoRNP assembly as human NUFIP

Protein-protein interaction

The PEP motif of AtNUFIP should direct its interaction with At15.5K. In Arabidopsis, At15.5K is encoded by three genes producing nearly identical proteins conserved with their human and yeast orthologues (Figure S1A). Considering that all three At15.5K genes are constitutively expressed (Figure S1B), we randomly chose At15.5K-3 (At4g22380) to test its interaction with AtNUFIP. We first tested their interaction by yeast two-hybrid analysis. The AtNUFIP and At15.5K ORFs were cloned by fusion with the binding (BD) and activating (AD) domains of GAL4. As a negative control, we used the GAL4 AD or BD empty vector. Cells co-transformed with different combinations of these constructs were grown in the presence or absence of histidine selectable marker. Clearly, yeast cells co-transformed with AD-AtNUFIP and BD-At15.5K (or BD-AtNUFIP and AD-At15.5K) could grow in the absence of histidine, revealing an interaction between these two proteins

Protein-protein interaction

Because VND7 is expected to form homo- and/or heterodimers with VND family proteins, including VND7 (Yamaguchi et al., 2008), these two bands may correspond to the VND7 homodimer-DNA complex (upper band) and the VND7 monomer-DNA complex

Protein-protein interaction

Investigation of a KNAT–BELL–OFP protein interaction network in a large-scale yeast two-hybrid screen showed the potential for KNAT7 to interact with a number of partner proteins including ... OFP4 ... Figure 1(a) shows that yeast cells expressing a KNAT7–DNA-binding domain (DBD) fusion and an OFP4–activation domain (AD) fusion interacted moderately well in this system, as judged by growth on both His− (which detects weak interactions) and Ura− (which detects stronger interactions) selective media, comparable to that of a positive control (MYB75–TT8 interaction

Protein-protein interaction

Co-transformation of truncated EYFP fusions to these genes revealed that co-expression of ... OFP4–C-EYFP with KNAT7–N-EYFP generated nuclear-localized fluorescence (Figure 2d,e). However, no fluorescence was detected when either the KNAT7–N-EYFP or OFP–C-EYFP construct was co-expressed with RACK1–C-EYFP and RACK1–N-EYFP, a non-interacting protein (RACK1, receptor for activated C kinase 1; Chen et al., 2006; Guo and Chen, 2008) that served as a negative control (Figure 2f; data not shown). These data indicate that ... OFP4 can interact with KNAT7 in vivo

Protein-protein interaction

Co-transformation of truncated EYFP fusions to these genes revealed that co-expression of OFP1–C-EYFP with KNAT7–N-EYFP ... generated nuclear-localized fluorescence (Figure 2d,e). However, no fluorescence was detected when either the KNAT7–N-EYFP or OFP–C-EYFP construct was co-expressed with RACK1–C-EYFP and RACK1–N-EYFP, a non-interacting protein (RACK1, receptor for activated C kinase 1; Chen et al., 2006; Guo and Chen, 2008) that served as a negative control (Figure 2f; data not shown). These data indicate that both OFP1 ... can interact with KNAT7 in vivo

Protein-protein interaction

When the WT Arabidopsis enzyme was examined by standard or blue native gel electrophoresis, a hexameric form was identified (Figures S4a and 1c). This was also the case for the P184L and the R176S–P184L mutants, suggesting that their reduced catalytic activities could not be ascribed to altered quaternary structure. When the G596R mutant was analyzed, it migrated as a smear, suggesting a lack of discrete structure

Protein-protein interaction

Initial proof of the interaction between AGG3 and AGB1 was provided by blue/white colony screening using the yeast two-hybrid (Y2H) system ... The interaction observed between AGG3 and AGB1 was abolished by the overexpression of either AGG1 or AGG2 in the same yeast cells, indicating that AGG1 and AGG2 compete with AGG3 for the same binding sites on AGB1 (Figure 2e). No interaction was detected between AGG3 and either AGG1, AGG2 or GPA1

Protein-protein interaction

We further confirmed the interaction of CO and AS1 by co-immunoprecipitation analysis using the Nicotiana benthamiana transient expression system. We found that AS1–hemagglutinin (HA) specifically co-immunoprecipitated with CO–GFP when both AS1–HA and CO–GFP were expressed in tobacco leaves

Protein-protein interaction

To verify the interaction observed in yeast, an in vitro binding assay was performed using a recombinant glutathione S-transferase (GST)-fused full length of CO protein and a full length of AS1 protein. More AS1 protein was precipitated with GST–CO than with GST alone (Figure 1d). We also performed another GST pull-down assay to confirm the result shown in Figure 1(c), and found that the truncated CO protein that contains only two B-box domains was sufficient for the interaction in vitro

Protein-protein interaction

Recent studies in yeast showed that Elongator associates with PCNA (Li et al., 2009), which implied that Elongator may have functions in PCNA-mediated DNA metabolism processes. The Arabidopsis genome contains two PCNA copies, PCNA1 and 2 ... ELO3 and DRL1 were co-localized with both PCNA1 and PCNA2 proteins in the same subcellular locations

Protein-protein interaction

Recent studies in yeast showed that Elongator associates with PCNA (Li et al., 2009), which implied that Elongator may have functions in PCNA-mediated DNA metabolism processes. The Arabidopsis genome contains two PCNA copies, PCNA1 and 2 ... ELO3 and DRL1 were co-localized with both PCNA1 and PCNA2 proteins in the same subcellular locations

Protein-protein interaction

Recent studies in yeast showed that Elongator associates with PCNA (Li et al., 2009), which implied that Elongator may have functions in PCNA-mediated DNA metabolism processes. The Arabidopsis genome contains two PCNA copies, PCNA1 and 2 ... ELO3 and DRL1 were co-localized with both PCNA1 and PCNA2 proteins in the same subcellular locations

Protein-protein interaction

Recent studies in yeast showed that Elongator associates with PCNA (Li et al., 2009), which implied that Elongator may have functions in PCNA-mediated DNA metabolism processes. The Arabidopsis genome contains two PCNA copies, PCNA1 and 2 ... ELO3 and DRL1 were co-localized with both PCNA1 and PCNA2 proteins in the same subcellular locations

Protein-protein interaction

we performed yeast two-hybrid assays by using AS2 as bait and TCP2, TCP4, TCP10 or TCP24 as prey. Our data showed that the co-expression of AS2 and each of these TCP genes, except TCP2, promoted expression of the ADE2 reporter gene

Protein-protein interaction

we performed a yeast two-hybrid screen to identify novel AS2-interacting proteins. We obtained approximately 300 positive clones from 2.5 · 106 screened library titers, and five of them correspond to TCP3 (At1g53230), a member of the class-II group of the TCP family (Martin-Trillo and Cubas, 2010

Protein-protein interaction

To verify the interaction between AS2 and TCPs, we performed glutathione-S-transferase (GST) pull-down assays using beads coated with the fusion protein GSTTCP2, GST-TCP3 or GST-TCP10. Transgenic plants expressing AS2-YFP or YFP under the estrogen inducible promoter (Zuo et al., 2000) were obtained, and total protein extracts from these transgenic plants were used in pull-down assays. As shown in the input lane, AS2-YFP (Figure 1b, central panel) and YFP (Figure 1b, right panel) were detected by an anti-GFP antibody. However, only AS2-YFP, but not YFP, was detected in the pull-down fractions by the GST-TCP2, GSTTCP3 or GST-TCP10 beads

Protein-protein interaction

we performed yeast two-hybrid assays by using AS2 as bait and TCP2, TCP4, TCP10 or TCP24 as prey. Our data showed that the co-expression of AS2 and each of these TCP genes, except TCP2, promoted expression of the ADE2 reporter gene

Protein-protein interaction

To verify the interaction between AS2 and TCPs, we performed glutathione-S-transferase (GST) pull-down assays using beads coated with the fusion protein GSTTCP2, GST-TCP3 or GST-TCP10. Transgenic plants expressing AS2-YFP or YFP under the estrogen inducible promoter (Zuo et al., 2000) were obtained, and total protein extracts from these transgenic plants were used in pull-down assays. As shown in the input lane, AS2-YFP (Figure 1b, central panel) and YFP (Figure 1b, right panel) were detected by an anti-GFP antibody. However, only AS2-YFP, but not YFP, was detected in the pull-down fractions by the GST-TCP2, GSTTCP3 or GST-TCP10 beads

Protein-protein interaction

To verify the interaction between AS2 and TCPs, we performed glutathione-S-transferase (GST) pull-down assays using beads coated with the fusion protein GSTTCP2, GST-TCP3 or GST-TCP10. Transgenic plants expressing AS2-YFP or YFP under the estrogen inducible promoter (Zuo et al., 2000) were obtained, and total protein extracts from these transgenic plants were used in pull-down assays. As shown in the input lane, AS2-YFP (Figure 1b, central panel) and YFP (Figure 1b, right panel) were detected by an anti-GFP antibody. However, only AS2-YFP, but not YFP, was detected in the pull-down fractions by the GST-TCP2, GSTTCP3 or GST-TCP10 beads

Protein-protein interaction

To test the interaction between AS2 and TCP3 in vivo, we generated a polyclonal antibody against TCP3, which recognizes both TCP3-YFP and TCP3 in western blot analysis (Figure S2). The nuclear fraction of 12-day-old Arabidopsis seedlings expressing YFP and AS2-YFP were incubated with protein-A beads coated with the anti-GFP antibody, and the immunoprecipitation products were analyzed by western blot using the anti-TCP3 antibody. Our results showed that TCP3 was detected only in the IP fraction from AS2-YFPexpressing plants, but not from YFP-expressing plants

Protein-protein interaction

we performed yeast two-hybrid assays by using AS2 as bait and TCP2, TCP4, TCP10 or TCP24 as prey. Our data showed that the co-expression of AS2 and each of these TCP genes, except TCP2, promoted expression of the ADE2 reporter gene

Protein-protein interaction

Protein-protein interaction

As we expected both paralogs to associate with U1-70K, we used Y2H assays using U1-70K full length, an N-terminal U1-70K (aa 1–172) and a C-terminal region (aa 179–427), each containing about half of the RRM, as fusions to the DNA-binding domain (Golovkin and Reddy, 1998) paired with U2AF35a as fusions to the activating domain. Earlier we had used these two halves of U1-70K to determine if the interaction between two SR proteins (RSZ21 and RSZ22) and U1-70K was in the region before the RRM or in the region following the RRM (Golovkin and Reddy, 1998). SR45 itself (along with SCL33) had been isolated in a Y2H screen using just the C-terminal part of U1-70K (Golovkin and Reddy, 1999). As shown in Figure 5(b), the U2AF35a paralog could interact with full-length U1-70K and with the N-terminal but not the C-terminal region, a finding that suggested that U2AF35a interacts with U1-70K somewhere in the N-terminal region. The negative BiFC results with U2AF35a could be due to instability of the complex or some post-translational modifications that occur in U2AF35a only in plant cells that might prevent interaction

Protein-protein interaction

To uncover its mode of action in splicing we searched for the interacting protein partners of SR45 by using it as bait in a Y2H screen. We screened about 50 000 transformants and identified 11 positive clones. U1-70K, a U1snRNP specific protein, which we reported previously to interact with SR45 (Golovkin and Reddy, 1999) ... interacting protein partner of SR45

Protein-protein interaction

To verify the interactions between SR45 and the U2AF35b ... we used in vitro pull-down assays with bacterially produced protein ... Expression clones as fusions to T7-tag were made for full-length U2AF35b, the N-terminally truncated U2AF35b isolated in the Y2H screen (U2AF35Ntrb), U2AF35b truncated at amino acid 250 to delete the C-terminal PSD (U2AF35Ctrb ... The SR45 construct was made previously as a fusion to S-tag ... As shown in Figure 1(c), all forms of the U2AF35 ... were pulled down by the SR45 bound to the beads

Protein-protein interaction

full-length U2AF35b and U2AF35bCtrb were cloned into a BiFC vector as fusions to the N-terminal region of YFP (YFPN). As we had a full-length U2AF35b clone we did not use the N-terminally truncated clone U2AF35bNtr but did use U2AF35bCtr as we were interested in seeing if the PSD influences the localization of the interacting proteins. SR45 had been cloned earlier into a BiFC vector as a fusion to the C-terminal region of YFP (SR45/YFPC ... Arabidopsis protoplasts were co-transfected with the SR45/YFPC construct and each of the U2AF35/YFPN constructs and examined for fluorescence. Figure 2 shows fluorescence observed in representative protoplasts transformed with SR45/YFPC and ... U2AF35b/YFPN or U2AF35Ctrb/YFPN. The fluorescence is seen mostly in nuclear speckles (concentrated loci of various sizes) with some fluorescence in the nucleoplasm (diffuse fluorescence) as has been shown previously to be the location of SR45 (Ali et al., 2008). The fluorescence resulting from the interaction of SR45/YFPC and U2AF35Ctrb/YFPN appeared in most cases to be in smaller speckles and more diffuse

Protein-protein interaction

To uncover its mode of action in splicing we searched for the interacting protein partners of SR45 by using it as bait in a Y2H screen. We screened about 50 000 transformants and identified 11 positive clones ... U2AF35b ... interacting protein partner of SR45 ... Control β-galactosidase assays for SR45 and the rescued U2AF35b construct alone showed no β-galactosidase activity whereas a double transformant with rescued U2AF35b and SR45 was positive for β-galactosidase activity (Figure 1a). As the isolated U2AF35b in the screen was truncated (aa 125–283), a full-length U2AF35b clone was cloned and its interaction with SR45 was tested using Y2H. Full-length U2AF35b was also shown to interact with SR45

Protein-protein interaction

to see if SR45 also interacts with U2AF35a we used in vitro pull-down assays with bacterially produced protein ... Expression clones as fusions to T7-tag were made for ... U2AF35a (amino acids 51–296 ... The SR45 construct was made previously as a fusion to S-tag ... U2AF35 ... pulled down by the SR45 bound to the beads

Protein-protein interaction

U2AF35a (amino acids 51-296 ... cloned into a BiFC vector as fusions to the N-terminal region of YFP (YFPN ... SR45 had been cloned earlier into a BiFC vector as a fusion to the C-terminal region of YFP (SR45/YFPC ... Arabidopsis protoplasts were co-transfected with the SR45/YFPC construct and each of the U2AF35/YFPN constructs and examined for fluorescence. Figure 2 shows fluorescence observed in representative protoplasts transformed with SR45/YFPC and U2AF35a/YFPN ... The fluorescence is seen mostly in nuclear speckles (concentrated loci of various sizes) with some fluorescence in the nucleoplasm (diffuse fluorescence) as has been shown previously to be the location of SR45

Protein-protein interaction

We generated recombinant protein in Escherichia coli and purified it to near homogeneity (Figure 5a). More VLN2 sedimented in the presence of actin filaments (Figure 5b, lane 4) compared to VLN2 alone (Figure 5b, lane 6) under high-speed centrifugation, suggesting that VLN2 binds to actin filaments. A dissociation constant value for the binding of VLN2 to actin filaments of 0.75 μm was calculated for the representative experiment in Figure 5(c), and a mean Kd of 1.3 ± 0.5 μm was determined from three independent experiments. Thus the VLN2 affinity for actin filaments is quite similar to that of VLN3 and VLN5 (Khurana et al., 2010; Zhang et al., 2010). We also determined VLN2 affinity for actin filaments in the presence of various concentrations of free calcium, and found that VLN2 binds to actin filaments with similar affinity across the physiological range of free calcium (Figure 5d).

Protein-protein interaction

We then performed a bimolecular fluorescence complementation (BiFC) assay to further confirm the AtISWI–RLT interaction in planta (Figure 5c). While plants carrying the 35Spro:YN-CHR11 and RLT2pro:RLT2-YC pair had clear YFP fluorescence in the nucleus, those harboring the 35Spro:YN and RLT2pro:RLT2-YC or the 35Spro:YN-CHR11 and RLT2pro:YC pair did not produce fluorescence

Protein-protein interaction

To test a possible in planta interaction between AtISWI and RLTs, we performed a co-immunoprecipitation (Co-IP) experiment to analyze the co-transformed tobacco leaves with either 35Spro:3×FLAG-CHR11 and RLT2pro:RLT2-TAP or 35Spro:3×FLAG-CHR11 and RLT2pro:TAP (Figure 5b). We used IgG sepharose to capture the RLT2-TAP or TAP, and the anti-FLAG antibody detected the 3× FLAG-CHR11 peptide by western blot from the RLT2-TAP-containing extracts, but not from the TAP-containing extracts

Protein-protein interaction

Y2H assays between SAMBA and six different mitotic cyclins (CYCA1;1, CYCA2;2, CYCA2;3, CYCA3;1, CYCB1;2, and CYCB2;2) revealed that SAMBA interacted with CYCA2;2 and CYCA2;3, weakly with CYCA1;1, and not with CYCA3;1, CYCB1;2, or CYCB2;2 (Fig. 4A). When the D-box in CYCA2;3 was deleted, no interaction with SAMBA was observed (Fig. 4B

Protein-protein interaction

Y2H assays between SAMBA and six different mitotic cyclins (CYCA1;1, CYCA2;2, CYCA2;3, CYCA3;1, CYCB1;2, and CYCB2;2) revealed that SAMBA interacted with CYCA2;2 and CYCA2;3, weakly with CYCA1;1, and not with CYCA3;1, CYCB1;2, or CYCB2;2 (Fig. 4A). When the D-box in CYCA2;3 was deleted, no interaction with SAMBA was observed (Fig. 4B). Fig. 4

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

Y2H assays between SAMBA and six different mitotic cyclins (CYCA1;1, CYCA2;2, CYCA2;3, CYCA3;1, CYCB1;2, and CYCB2;2) revealed that SAMBA interacted with CYCA2;2 and CYCA2;3, weakly with CYCA1;1, and not with CYCA3;1, CYCB1;2, or CYCB2;2 (Fig. 4A). When the D-box in CYCA2;3 was deleted, no interaction with SAMBA was observed (Fig. 4B

Protein-protein interaction

Therefore, we performed yeast two-hybrid (Y2H) assays with the SAMBA protein against all APC/C subunits identified in Arabidopsis and its two coactivators, CCS52A2 and CCS52B. The results revealed a direct interaction of SAMBA with APC3b (Fig. S1A) but not with APC1, APC2, APC3a, APC4, APC5, APC6, APC7, APC8, APC10, APC11, or the activators CCS52A2 and CCS52B. Taken together, the protein interaction data indicate that SAMBA is a component of the APC/C complex in plants, by binding APC3b

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

subunits APC1, APC2, APC3b, APC4, APC5, APC6, APC7, APC8, and APC10 ... TAP was carried out with 6-d-old SAMBA-expressing seedlings C-terminally fused to the GS tag (see SI Materials and Methods) and proteins were identified by mass spectrometry (MS). In agreement with previous results, SAMBA interacted with all APC/C subunits in planta, except APC11, which is difficult to identify with the selected analytical approach because of its small size (Table S1). Also, the interaction with the activator CCS52A2 was found, but not with CCS52B, UVI4, and UVI4-like/OSD1/GIG1

Protein-protein interaction

For the BiFC assays, WRKY8 was fused to the C-terminal yellow fluorescent protein (YFP) fragment (WRKY8-C-YFP) and VQ9 to the N-terminal YFP fragment (VQ9-N-YFP). When fused, WRKY8-C-YFP was co-expressed with VQ9-N-YFP in leaves of Nicotiana benthamiana (tobacco), and the YFP signal was detected in the nuclear compartment of transformed cells, as revealed by staining with 4',6-diamidino-2-phenylindole (DAPI) (Figures 4b and S1a). We did not detect any fluorescence in the negative controls

Protein-protein interaction

The Gal4 transcription activation-based yeast two-hybrid system was used. The WRKY8 full-length cDNA with a deleted activation domain was fused to the Gal4 DNA-binding domain of the bait vector (BD-WRKY8). After screening, three independent clones encoding VQ9 were identified by prototrophy for His and Ade. To confirm the interaction, the full-length VQ9 cDNA was cloned and introduced into the prey vector (AD-VQ9). The BD-WRKY8 and AD-VQ9 plasmids were co-transformed into yeast and the interaction was reconstructed

Protein-protein interaction

VQ9 interacted with the WRKY8 fragment that overlapped with its DNA-binding domain, we anticipated that the physical interaction may interfere with the DNA-binding activity of WRKY8. To test this possibility, we generated recombinant proteins in Escherichia coli and tested the WRKY8 binding activity to an oligonucleotide harboring two direct TTGACC W-box repeats (Pr; Figure 6a) using electrophoretic mobility shift assay (EMSA). Protein–DNA complexes with reduced migration were detected when WRKY8 was incubated with the DNA probe (Figure 6b); however, when the W-box sequences in the probes were changed from TTGACC to TTGAAC (mPr; Figure 6a), no binding complexes were detected (Figure 6b). These results suggested that the binding of WRKY8 to the W-box sequences is highly specific. When WRKY8 was combined with VQ9 in the binding reactions, we observed the formation of a super-shifted band with significantly lower intensity (Figure 6b). Moreover, when the protein level of VQ9 was doubled (2 × VQ9) in the assay, no visibly retarded band was observed (Figure 6b). Thus, the WRKY8–VQ9 interaction decreased the DNA-binding activity of WRKY8

Protein-protein interaction

BSK1 ... efficiently phosphorylated by MBP–BIN2 ... but not by MBP–BIN2K69R ... Next, we tested whether Ser230, the major site of BSK1 phosphorylated by BRI1 (Figure 6) (Tang et al., 2008), is also a BSK1 phosphorylation site for BIN2 and BIL2. As shown in Figure 9(b), both GST–BSK1 and GST–BSK1S230A were equally phosphorylated by MBP–BIN2, as well as by GST–BIL2. This suggests that BSKs are phosphorylated on a residue other than Ser230, and are thus differentially modified by BRI1 and GSK3-like kinases

Protein-protein interaction

GST–BSKs were phosphorylated by MBP–BRI1-KD, as previously observed for ... GST–BSK3 ... BRI1 phosphorylated BSKs with similar efficiency with the exception of BSK3, which served as a weak phosphorylation substrate

Protein-protein interaction

BSK1 ... efficiently phosphorylated by ... GST–BIL2 ... but not by ... GST–BIL2K99R ... Next, we tested whether Ser230, the major site of BSK1 phosphorylated by BRI1 (Figure 6) (Tang et al., 2008), is also a BSK1 phosphorylation site for BIN2 and BIL2. As shown in Figure 9(b), both GST–BSK1 and GST–BSK1S230A were equally phosphorylated by MBP–BIN2, as well as by GST–BIL2. This suggests that BSKs are phosphorylated on a residue other than Ser230, and are thus differentially modified by BRI1 and GSK3-like kinases

Protein-protein interaction

The known interaction between BRI1 and BSK1 (Tang et al., 2008) was utilized as a positive control in these experiments. Epidermal cells of Nicotiana benthamiana leaves co-expressing BRI1 fused to the N-terminal half of YFP (nYFP) and BSK1 ... fused to the C-terminal half of YFP (cYFP) showed a strong fluorescence signal

Protein-protein interaction

After transient expression in BY–2 tobacco protoplasts using bimolecular fluorescence complementation (BiFC), YFP fluorescence was detected in several protoplasts, demonstrating that AtSnRK1a1 and AtKRP6 are interacting partners in vivo. In addition, this interaction only occurred in the nucleus

Protein-protein interaction

had been established previously by a two-hybrid approach that AtKRP6 interacts with A. thaliana CDKA;1 (De Veylder et al., 2001). As shown in Figure 5(a), AtKRP6T152D and AtKRP6WT interact to a similar degree with AtCDKA;1–AF, the AtCDKA;1 variant

Protein-protein interaction

We then tested the interaction of AtKRP6WT and AtKRP6T152D with a D–type cyclin, the second partner in the CDK/cyclin complex, which was previously shown to be a true partner of AtKRP6 in planta (Van Leene et al., 2007). Interestingly, the phosphorylation-mimetic form AtKRP6T152D partially lost its ability to interact with its cyclin partner

Protein-protein interaction

we conducted a bimolecular fluorescence complementation (BiFC) analysis to analyze their interactions. Both the N-terminal and C-terminal halves of YFP were fused to FHY3/CPD45 and the fusions were transiently expressed in Nicotiana benthamiana (tobacco) leaf cells by Agrobacterium tumefaciens-mediated transformation ... YFP signals were observed in the cells co-transformed with NYFP-CPD45 and CYFP-CPD45, suggesting that FHY3/CPD45 can self-interact

Protein-protein interaction

we conducted a bimolecular fluorescence complementation (BiFC) analysis ... In tobacco leaf cells co-transformed with NYFP-CPD45 and CYFP-CPD25 or NYFP-CPD25 and CYFP-CPD45, YFP signals were also observed and co-localized with the DAPI staining (Figure 10a), suggesting that FHY3/CPD45 and FRS4/CPD25 form a heterodimer in the nucleus

Protein-protein interaction

BOP1:Flag ... fractionated on a 10–50% sucrose density gradient. After ultracentrifugation, fractions were collected, and immunoblot analysis was performed with anti-Flag ... another immunoblot analysis was performed with antibodies against the 60S ribosomal protein L10a, which is associated with 60S ribosomal large subunits, 80S monosomes, and polysomes ... BOP1 ... most abundant in the fractions that contained 60S large subunits and 80S monosomes, suggesting ribosomal association of these proteins

Protein-protein interaction

We used BiFC to test for an interaction of ... Arabidopsis BOP1 and WDR12 in plant cells ... Using agroinfiltration ... BOP1, and WDR12 cDNAs were expressed in combination in N. benthamiana leaves as YFPN- and YFPC fusion proteins for confocal laser scanning microscopy ... resulted in strong YFP fluorescence in the nucleolus, indicating that ... BOP1, and WDR12 interact with each other in the nucleolus

Protein-protein interaction

we conducted co-immunoprecipitation assays ... The following pairs were co-expressed in N. benthamiana leaves by agroinfiltration ... AtPES:Flag and Myc-fused BOP1 ... AtPES:Flag was co-immunoprecipitated with ... BOP1:Myc

Protein-protein interaction

AtPES:Flag ... fractionated on a 10–50% sucrose density gradient. After ultracentrifugation, fractions were collected, and immunoblot analysis was performed with anti-Flag ... another immunoblot analysis was performed with antibodies against the 60S ribosomal protein L10a, which is associated with 60S ribosomal large subunits, 80S monosomes, and polysomes ... AtPES ... most abundant in the fractions that contained 60S large subunits and 80S monosomes, suggesting ribosomal association of these proteins

Protein-protein interaction

we conducted co-immunoprecipitation assays ... The following pairs were co-expressed in N. benthamiana leaves by agroinfiltration ... BOP1:Flag and WDR12:HA ... BOP1:Flag was co-immunoprecipitated with WDR12:HA

Protein-protein interaction

We used BiFC to test for an interaction of AtPES with Arabidopsis BOP1 ... Using agroinfiltration, AtPES, BOP1 ... were expressed in combination in N. benthamiana leaves as YFPN- and YFPC fusion proteins for confocal laser scanning microscopy ... resulted in strong YFP fluorescence in the nucleolus, indicating that AtPES, BOP1 ... interact with each other in the nucleolus

Protein-protein interaction

WDR12:HA ... fractionated on a 10–50% sucrose density gradient. After ultracentrifugation, fractions were collected, and immunoblot analysis was performed with ... anti-HA ... another immunoblot analysis was performed with antibodies against the 60S ribosomal protein L10a, which is associated with 60S ribosomal large subunits, 80S monosomes, and polysomes ... WDR12 ... most abundant in the fractions that contained 60S large subunits and 80S monosomes, suggesting ribosomal association of these proteins. Interestingly, WDR12 was also detected in the lighter fractions of the gradient, suggesting that WDR12 may be loosely associated with the PeBOW complex or may be involved in other cellular processes

Protein-protein interaction

We used BiFC to test for an interaction of AtPES with ... WDR12 in plant cells ... Using agroinfiltration, AtPES ... and WDR12 cDNAs were expressed in combination in N. benthamiana leaves as YFPN- and YFPC fusion proteins for confocal laser scanning microscopy ... resulted in strong YFP fluorescence in the nucleolus, indicating that AtPES ... and WDR12 interact with each other in the nucleolus

Protein-protein interaction

To confirm this interaction in vivo, either AtMBP-1–YFP and Flag-AtSAP5, or LOS2–YFP and Flag-AtSAP5 were expressed in Nicotiana benthamiana by agro-infiltration. Protein extracts isolated from the N. benthamiana were subjected to co-immunoprecipitation (Co-IP) assays. Either AtMBP-1–YFP or LOS2–YFP fusion proteins were immunoprecipitated from the plant extracts using the anti-GFP agarose. Flag-AtSAP5 was detected in the AtMBP-1–YFP:Flag-AtSAP5 immunocomplex using the anti-Flag antibody Figure 1(d). By contrast, no signal was detected in reactions using LOS2–YFP and Flag-AtSAP5

Protein-protein interaction

To confirm this interaction in plant cells, biomolecular fluorescence complementation (BiFC) analysis was performed by co-infiltrating constructs that encode nYFP-AtSAP5 and AtMBP-1-cYFP into N. benthamiana. Fluorescence signal, indicating interaction between nYFP-AtSAP5 and AtMBP-1-cYFP, was detected in cells of the agro-infiltrated tissue within a nuclear subcompartment, possibly corresponding with the nucleolus

Protein-protein interaction

In order to identify potential interacting partners of AtSAP5, yeast two-hybrid screening was conducted using AtSAP5 as bait and an Arabidopsis cDNA library as prey. From this screening, 36 cDNA clones were obtained and sequence analysis indicated that six of these cDNAs represented transcripts derived from the LOS2 gene ... This finding raised the possibility that, as in mammalian cells, an Arabidopsis MBP-1-like protein (AtMBP-1) could be produced as an alternative translation product of the LOS2 gene. To determine which of these putative gene products interacts with AtSAP5, specific yeast two-hybrid assays were performed. For this assay, LOS2 and AtMBP-1 coding sequences were cloned into both bait (pGBKT7) and prey (pGADT7) yeast vectors, and each construct was co-transformed into yeast cells with a complementary AtSAP5 construct Figure 1(a). Yeast cells transformed with vectors that co-express AtMBP-1 and AtSAP5 proteins grew well under high stringency conditions, while yeast cells transformed with LOS2/enolase and AtSAP5 did not, indicating strong interaction between AtSAP5 and AtMBP-1 but not between AtSAP5 and LOS2/enolase

Protein-protein interaction

The interaction between AtMBP-1 and AtSAP5 identified through yeast two-hybrid assays was verified with in vitro protein pull-down assays Figure 1(c). His-Trx-AtMBP-1, His-LOS2, and GST-AtSAP5 constructs were transformed into Escherichia. coli and the expressed proteins purified using either His-or GST resin, respectively. His-Trx-AtMBP-1 or His-LOS2 fusion proteins were incubated with the GST-AtSAP5 fusion protein and, after extensive washing, the bound proteins were eluted from the GST resin by reduced glutathione. The eluted proteins were analyzed on immuno-blots probed with anti-His and anti-GST antibodies. Consistent with the results of yeast two- hybrid assay, His-Trx-AtMBP-1 was pulled down by GST-AtSAP5, while His-LOS2 did not bind effectively to GST-AtSAP5

Protein-protein interaction

protoplasts were co-transfected with c–Myc- and HA-tagged isoforms, immunoprecipitated with antisera against one of the epitope tags, and probed with antisera directed against the alternative epitope tag in Western blots of SDS–PAGE gels ... ABCG11 formed an apparent homodimer as described previously (McFarlane et al., 2010

Protein-protein interaction

protoplasts were co-transfected with c–Myc- and HA-tagged isoforms, immunoprecipitated with antisera against one of the epitope tags, and probed with antisera directed against the alternative epitope tag in Western blots of SDS–PAGE gels ... ABCG9 also formed an apparent homodimer

Protein-protein interaction

protoplasts were co-transfected with c–Myc- and HA-tagged isoforms, immunoprecipitated with antisera against one of the epitope tags, and probed with antisera directed against the alternative epitope tag in Western blots of SDS–PAGE gels ... ABCG14 formed an apparent heterodimer with ABCG11

Protein-protein interaction

protoplasts were co-transfected with c–Myc- and HA-tagged isoforms, immunoprecipitated with antisera against one of the epitope tags, and probed with antisera directed against the alternative epitope tag in Western blots of SDS–PAGE gels ... ABCG9 formed an apparent heterodimer with ABCG11

Protein-protein interaction

For yeast three-hybrid assays, TT2, PAP1 and PAP2 were individually fused to the activation domain (AD-TT2, AD-PAP1 and AD-PAP2), and the pBRIDGE vector with only the TT8 integration was used as a control (BD-TT8). Consistent with previous reports (Zimmermann et al., 2004), protein interactions between each of the three R2R3-MYBs and TT8 were observed for each of the three control experiments lacking TCP3 expression, with interaction strengths varying from 54.45 to 69.23 Miller units (Figure 4h). However, co-expression of TCP3 with TT8 and each of the three tested R2R3-MYB genes led to significantly enhanced reporter activity (93.62–107.51 Miller units; Figure 4h), suggesting that TCP3 influences the stability of the MBW complex and thereby enhances its transcriptional activation activity

Protein-protein interaction

For yeast three-hybrid assays, TT2, PAP1 and PAP2 were individually fused to the activation domain (AD-TT2, AD-PAP1 and AD-PAP2), and the pBRIDGE vector with only the TT8 integration was used as a control (BD-TT8). Consistent with previous reports (Zimmermann et al., 2004), protein interactions between each of the three R2R3-MYBs and TT8 were observed for each of the three control experiments lacking TCP3 expression, with interaction strengths varying from 54.45 to 69.23 Miller units (Figure 4h). However, co-expression of TCP3 with TT8 and each of the three tested R2R3-MYB genes led to significantly enhanced reporter activity (93.62–107.51 Miller units; Figure 4h), suggesting that TCP3 influences the stability of the MBW complex and thereby enhances its transcriptional activation activity

Protein-protein interaction

For yeast three-hybrid assays, TT2, PAP1 and PAP2 were individually fused to the activation domain (AD-TT2, AD-PAP1 and AD-PAP2), and the pBRIDGE vector with only the TT8 integration was used as a control (BD-TT8). Consistent with previous reports (Zimmermann et al., 2004), protein interactions between each of the three R2R3-MYBs and TT8 were observed for each of the three control experiments lacking TCP3 expression, with interaction strengths varying from 54.45 to 69.23 Miller units (Figure 4h). However, co-expression of TCP3 with TT8 and each of the three tested R2R3-MYB genes led to significantly enhanced reporter activity (93.62–107.51 Miller units; Figure 4h), suggesting that TCP3 influences the stability of the MBW complex and thereby enhances its transcriptional activation activity

Protein-protein interaction

To test whether ATML1 and PDF2 are capable of dimerization, we crossing all the tagged lines described above to generate transgenic plants expressing combinations of FLAG and GFP-tagged ATML1 and PDF2 proteins. Using co-immunoprecipitation, we were able to demonstrate ... heterodimerization of PDF2 with ATML1 in planta

Protein-protein interaction

To test whether ATML1 and PDF2 are capable of dimerization, we crossing all the tagged lines described above to generate transgenic plants expressing combinations of FLAG and GFP-tagged ATML1 and PDF2 proteins. Using co-immunoprecipitation, we were able to demonstrate homodimerization of PDF2

Protein-protein interaction

To confirm the in vivo interaction of BES1 and HAT1, we performed a BiFC experiment with HAT1 fused to N-terminal YFP (HAT1-nYFP) and BES1 fused to C-terminal YFP (BES1-cYFP). When the constructs were co-transformed into tobacco leaves, strong fluorescence signals were observed in the nuclei (Figure 5d). As a negative control, we co-transformed HAT1-nYFP and cYFP and there was no detectable fluorescence signal (Figure 5c). These results indicated that HAT1 interacts with BES1 in vivo

Protein-protein interaction

Bimolecular fluorescence complementation (BiFC) assay was performed in tobacco leaves. BIN2 fused with the C-terminus of yellow fluorescent protein (BIN2–cYFP) interacted with HAT1 fused with the N-terminus of YFP (HAT1–nYFP), leading to the reconstruction of YFP, as fluorescence was detected in cells co-transformed with the corresponding constructs (Figure 3d). No fluorescence was detected in the negative control, in which cYFP plasmid was co-transformed with the HAT1–nYFP plasmid (Figure 3c). These results indicated that HAT1 and BIN2 interact with each other in vitro and in vivo

Protein-protein interaction

We tested if BIN2 could directly interact with HAT1. Glutathione S-transferase (GST)–BIN2 and maltose binding protein (MBP)–HAT1 fusion proteins were expressed in E. coli and purified. First, GST–BIN2 was used to pull-down MBP–HAT1 protein, which can be detected by an anti-MBP antibody. While GST protein alone did not pull-down MBP–HAT1, GST–BIN2 did, indicating an interaction between BIN2 and HAT1

Protein-protein interaction

ABC1K1 phosphorylates the tocopherol cyclase ... the mature kinase was produced in a cell-free rabbit reticulocyte lysate and used in kinase assays in the presence or absence of the purified VTE1 and [γ–33P]ATP. The reticulocyte lysate is highly concentrated, containing a large variety of proteins including kinases and their substrates. Therefore, it was used as a negative control in the absence of added substrates and ABC1K1 kinase. In this reaction several weak bands were observed in the background (Figure 7a, IVTmix). In phosphorylation reactions containing both the purified VTE1 and the ABC1K1 in vitro product, a significant incorporation of 33P (Figure 7a,b) was detected in a protein band at around 45 kDa that was absent from the control reactions (Figure 7a, IVTmix, ABC1K1 and VTE1). The mass of the phosphoprotein was similar to the predicted mass of VTE1 (43.5 kDa ... In parallel, western blotting was performed using αABC1K1 or αVTE1 antibodies. The 45–kDa phosphoprotein co-migrated with the band detected by αVTE1, strongly supporting that VTE1 was the phosphoprotein

Protein-protein interaction

To determine whether these interactions also occur in plant cells, we then employed the bimolecular fluorescence complementation (BiFC) system. Full-length JAZ4 ... fused to the N-terminal region of the yellow fluorescent protein (YFP). Agrobacterial cells harboring the corresponding interaction pair were infiltrated into tobacco (Nicotiana benthamiana) leaves. In parallel, empty vectors in combination with each fusion construct were coinfiltrated into tobacco leaves. After 2 d of incubation, YFP signals were observed with fluorescence microscopy. The samples coinfiltrated with an interaction pair showed YFP fluorescence in the cell nuclei, whereas all control samples failed to give any YFP signal (Figure 3C). These results indicated that WRKY57 and its partners colocalize and interact in plant cell nuclei

Protein-protein interaction

We further tested their interaction in vitro by protein pull-down assays. Myc-WRKY57 and HA-JAZ4 ... were coexpressed in yeast cells. The protein complexes were incubated with anti-HA and A/G-agarose beads and then separated on SDS-PAGE for immunoblotting with anti-Myc antibody. As a result, the JAZ4 ... could be pulled down by WRKY57

Protein-protein interaction

To search for potential partners of the WRKY57 protein, we employed the yeast two-hybrid system. WRKY57 was fused with the BD domain of the pGBK-T7 vector as bait. Yeast cells harboring the bait were transformed with a cDNA library containing inserts for prey proteins fused to GAL4-AD. In total, 47 colonies were positive for the expression of the His3 and LacZ reporter genes. Among these candidate interactors ... IAA29 were frequently represented. To confirm their interaction in yeast, their open reading frame sequences were fused with the AD domain of the pGAD-T7 vector and used for further interaction experiments with WRKY57 ... WRKY57 strongly interacted with ... IAA29

Protein-protein interaction

To determine whether these interactions also occur in plant cells, we then employed the bimolecular fluorescence complementation (BiFC) system. Full-length ... JAZ8 ... fused to the N-terminal region of the yellow fluorescent protein (YFP). Agrobacterial cells harboring the corresponding interaction pair were infiltrated into tobacco (Nicotiana benthamiana) leaves. In parallel, empty vectors in combination with each fusion construct were coinfiltrated into tobacco leaves. After 2 d of incubation, YFP signals were observed with fluorescence microscopy. The samples coinfiltrated with an interaction pair showed YFP fluorescence in the cell nuclei, whereas all control samples failed to give any YFP signal (Figure 3C). These results indicated that WRKY57 and its partners colocalize and interact in plant cell nuclei

Protein-protein interaction

To determine whether these interactions also occur in plant cells, we then employed the bimolecular fluorescence complementation (BiFC) system. Full-length ... IAA29 ... fused to the N-terminal region of the yellow fluorescent protein (YFP). Agrobacterial cells harboring the corresponding interaction pair were infiltrated into tobacco (Nicotiana benthamiana) leaves. In parallel, empty vectors in combination with each fusion construct were coinfiltrated into tobacco leaves. After 2 d of incubation, YFP signals were observed with fluorescence microscopy. The samples coinfiltrated with an interaction pair showed YFP fluorescence in the cell nuclei, whereas all control samples failed to give any YFP signal (Figure 3C). These results indicated that WRKY57 and its partners colocalize and interact in plant cell nuclei

Protein-protein interaction

To search for potential partners of the WRKY57 protein, we employed the yeast two-hybrid system. WRKY57 was fused with the BD domain of the pGBK-T7 vector as bait. Yeast cells harboring the bait were transformed with a cDNA library containing inserts for prey proteins fused to GAL4-AD. In total, 47 colonies were positive for the expression of the His3 and LacZ reporter genes. Among these candidate interactors ... JAZ8 ... were frequently represented. To confirm their interaction in yeast, their open reading frame sequences were fused with the AD domain of the pGAD-T7 vector and used for further interaction experiments with WRKY57 ... WRKY57 strongly interacted with ... JAZ8

Protein-protein interaction

To search for potential partners of the WRKY57 protein, we employed the yeast two-hybrid system. WRKY57 was fused with the BD domain of the pGBK-T7 vector as bait. Yeast cells harboring the bait were transformed with a cDNA library containing inserts for prey proteins fused to GAL4-AD. In total, 47 colonies were positive for the expression of the His3 and LacZ reporter genes. Among these candidate interactors, JAZ4 ... were frequently represented. To confirm their interaction in yeast, their open reading frame sequences were fused with the AD domain of the pGAD-T7 vector and used for further interaction experiments with WRKY57 ... WRKY57 strongly interacted with JAZ4

Protein-protein interaction

We further tested their interaction in vitro by protein pull-down assays. Myc-WRKY57 and HA ... IAA29 were coexpressed in yeast cells. The protein complexes were incubated with anti-HA and A/G-agarose beads and then separated on SDS-PAGE for immunoblotting with anti-Myc antibody. As a result, the ... IAA29 ... could be pulled down by WRKY57

Protein-protein interaction

We further tested their interaction in vitro by protein pull-down assays. Myc-WRKY57 and HA ... JAZ8 ... were coexpressed in yeast cells. The protein complexes were incubated with anti-HA and A/G-agarose beads and then separated on SDS-PAGE for immunoblotting with anti-Myc antibody. As a result, the ... JAZ8 ... could be pulled down by WRKY57

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... several plant homologs of SWI/SNF complex subunits were repeatedly purified from cell culture and seedlings, including ... SWI3C

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... detected in all experiments ... At5g55210

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... ARP7 ... detected in all experiments

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... SWI3D ... isolated from seedlings as well

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... several plant homologs of SWI/SNF complex subunits were repeatedly purified from cell culture and seedlings, including ... BRM

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... several plant homologs of SWI/SNF complex subunits were repeatedly purified from cell culture and seedlings, including ... ARP7

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... SWP73A ... isolated from seedlings as well

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... detected in all experiments ... At5g17510

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... several plant homologs of SWI/SNF complex subunits were repeatedly purified from cell culture and seedlings, including SYD

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... ARP4 ... detected in all experiments

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... several plant homologs of SWI/SNF complex subunits were repeatedly purified from cell culture and seedlings, including ... SWP73B

Protein-protein interaction

To identify additional interacting partners of AN3 besides the GRFs, AN3 was used as a bait for tandem affinity purification (TAP) followed by mass spectrometry analysis (TAP/MS), a powerful method to isolate and identify protein complexes (Van Leene et al., 2007; see Methods for experimental details). Both C- and N-terminal fusions of AN3 to the GS TAP tag were expressed under the control of the 35S promoter in Arabidopsis cell cultures. Eight independent TAP experiments resulted in the identification of 14 proteins, including AN3 (Table 2). Furthermore, TAP from 6-d-old Arabidopsis seedlings expressing C-terminal GS-tagged AN3 from the CDKA;1 promoter confirmed 11 out of the 14 proteins previously isolated from cell cultures ... several plant homologs of SWI/SNF complex subunits were repeatedly purified from cell culture and seedlings, including ... ARP4

Protein-protein interaction

We performed a co-immunoprecipitation (Co-IP) experiment to confirm the interaction between YID1/MED16 and MED25. Green fluorescence protein-tagged YID1/MED16 and myc-tagged MED25 were co-filtrated into the leaves of N. benthamiana, with total proteins extracted for the Co-IP analyses. The results showed that GFP-MED16 were co-immunoprecipitated with myc-MED25 (Figure 3d), suggesting that YID1/MED16 interacts with MED25 in vivo

Protein-protein interaction

To confirm the interaction between YID1/MED16 and MED25 in vivo, we conducted a bimolecular fluorescent complementation (BiFC) analysis. We generated two constructs, nYFP-MED16 and cCFP-MED25, and co-transformed them into the leaf cells of Nicotiana benthamiana. Strong GFP signals were observed in the combination of nYFP-MED16 and cCFP-MED25 (Figure 3c), with no GFP signals being detected in the combinations of nYFP-MED16 with the empty vector cCFP or cCFP-MED25 with the empty vector nYFP

Protein-protein interaction

To confirm the interactions between MED25 and EIN3/EIL1, we carried out a BiFC analysis. We co-transformed the nYFP-MED25 with cCFP-EIN3 or cCFP-EIL1 into the leaves of N. benthamiana. The obvious fluorescence in the nuclei was observed in both combinations of nYFP-MED25/cCFP-EIN3 and nYFP-MED25/cCFP-EIL1 (Figures 5b and S5), suggesting that MED25 interacts with EIN3/EIL1 in vivo. This BiFC result was supported by the firefly luciferase (LUC) complementation imaging (LCI) assay (Chen et al., 2008). The constructs MED25-nLuc and cLuc-EIN3/EIL1 were generated and co-infiltrated into N. benthamiana leaves. The LUC activity signal was detected between MED25-nLuc and cLuc-EIN3/EIL1

Protein-protein interaction

To confirm the interactions between MED25 and EIN3/EIL1, we carried out a BiFC analysis. We co-transformed the nYFP-MED25 with cCFP-EIN3 or cCFP-EIL1 into the leaves of N. benthamiana. The obvious fluorescence in the nuclei was observed in both combinations of nYFP-MED25/cCFP-EIN3 and nYFP-MED25/cCFP-EIL1 (Figures 5b and S5), suggesting that MED25 interacts with EIN3/EIL1 in vivo. This BiFC result was supported by the firefly luciferase (LUC) complementation imaging (LCI) assay (Chen et al., 2008). The constructs MED25-nLuc and cLuc-EIN3/EIL1 were generated and co-infiltrated into N. benthamiana leaves. The LUC activity signal was detected between MED25-nLuc and cLuc-EIN3/EIL1

Protein-protein interaction

We immunoprecipitated the GIF1 complex using anti-GFP antibodies from inflorescences and analyzed the output by LC-MS/MS followed by label-free protein quantification analysis ... many components necessary to generate a functional SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complex were identified in our pull downs (Table 1), including three different ATPases of the SWI/SNF family ... SPLAYED (SYD

Protein-protein interaction

We immunoprecipitated the GIF1 complex using anti-GFP antibodies from inflorescences and analyzed the output by LC-MS/MS followed by label-free protein quantification analysis ... many components necessary to generate a functional SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complex were identified in our pull downs (Table 1), including three different ATPases of the SWI/SNF family ... CHR12

Protein-protein interaction

We immunoprecipitated the GIF1 complex using anti-GFP antibodies from inflorescences and analyzed the output by LC-MS/MS followed by label-free protein quantification analysis ... On the other hand, we found that GIF1 mainly interacted with two GRFs in our system, GRF5

Protein-protein interaction

We immunoprecipitated the GIF1 complex using anti-GFP antibodies from inflorescences and analyzed the output by LC-MS/MS followed by label-free protein quantification analysis ... many components necessary to generate a functional SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complex were identified in ... including ... SWP73A (SWI/SNF ASSOCIATED PROTEIN 73A

Protein-protein interaction

We immunoprecipitated the GIF1 complex using anti-GFP antibodies from inflorescences and analyzed the output by LC-MS/MS followed by label-free protein quantification analysis ... many components necessary to generate a functional SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complex were identified in our pull downs (Table 1), including three different ATPases of the SWI/SNF family: BRAHMA (BRM

Protein-protein interaction

We immunoprecipitated the GIF1 complex using anti-GFP antibodies from inflorescences and analyzed the output by LC-MS/MS followed by label-free protein quantification analysis ... On the other hand, we found that GIF1 mainly interacted with two GRFs in our system ... GRF3

Protein-protein interaction

To identify potential upstream MAP kinase kinase interaction partner(s) of AtMPK10, we employed the yeast two-hybrid interaction system. All 10 known Arabidopsis MKKs were fused to the GAL4 binding domain and confirmed to mediate no auto-activation of the β-galactosidase (β-GAL) reporter system. In the presence of AtMPK10, only AtMKK2 but not the other nine MAPKKs triggered activation of the two-hybrid system ( Figure 2B). This indicated that AtMPK10 interacts specifically with AtMKK2 and no other upstream Arabidopsis MKK

Protein-protein interaction

In addition, we tested interaction between VCC and OPS by a bimolecular fluorescence complementation assay. We coexpressed VCC fused to the C-terminal portion of yellow fluorescent protein (YFP; CY-VCC) and OPS fused to the N terminus of YFP (NY-OPS) in Arabidopsis protoplasts (Fig. 8B). As negative controls, we coexpressed each of the fusion proteins with the corresponding empty vector and the two empty vectors together (Fig. 8B). Only the coexpression of CY-VCC and NY-OPS allowed for the reconstitution of YFP fluorescence above background levels (Fig. 8B), indicating that the two proteins are able to interact in Arabidopsis

Protein-protein interaction

We cotransformed yeast cells with pBT3-C-OPS and pPR3-N-VCC, pBT3-C and pPR3-N VCC, or pBT3-C-OPS and pPR3-N and determined the number of transformant colonies grown on plates with selection medium for interaction (-Leu, Trp, His [-LWH] plus 15 mm 3-aminotriazole [3-AT]) and colonies grown on plates with section medium for plasmid transformation (-Leu, Trp [-LW]) to calculate a ratio (Fig. 8A). The coexpression of VCC as prey and OPS as bait resulted in 24% colony growth under selection for interaction, whereas we detected 0% and 9% colony growth when VCC and OPS, respectively, were coexpressed with empty vector OPS (Fig. 8A